title: The phylogenetic utility of chloroplast and nuclear DNA markers and the phylogeny of the Rubiaceae tribe Spermacoceae.
abstract: The phylogenetic utility of chloroplast (atpB-rbcL, petD, rps16, trnL-F) and nuclear (ETS, ITS) DNA regions was investigated for the tribe Spermacoceae of the coffee family (Rubiaceae). ITS was, despite often raised cautions of its utility at higher taxonomic levels, shown to provide the highest number of parsimony informative characters, in partitioned Bayesian analyses it yielded the fewest trees in the 95% credible set, it resolved the highest proportion of well resolved clades, and was the most accurate region as measured by the partition metric and the proportion of correctly resolved clades (well supported clades retrieved from a combined analysis regarded as "true"). For Hedyotis, the nuclear 5S-NTS was shown to be potentially as useful as ITS, despite its shorter sequence length. The chloroplast region being the most phylogenetically informative was the petD group II intron. We also present a phylogeny of Spermacoceae based on a Bayesian analysis of the four chloroplast regions, ITS, and ETS combined. Spermacoceae are shown to be monophyletic. Clades supported by high posterior probabilities are discussed, especially in respect to the current generic classification. Notably, Oldenlandia is polyphyletic, the two subgenera of Kohautia are not sister taxa, and Hedyotis should be treated in a narrow sense to include only Asian species.
authors.affiliation: Bergius Foundation, Royal Swedish Academy of Sciences and Botany Department, Stockholm University, SE-106 91 Stockholm, Sweden. jesper@bergianska.se
authors.forename: Jesper
authors.initials: J
authors.lastname: Kårehed
authors.forename: Inge
authors.initials: I
authors.lastname: Groeninckx
authors.forename: Steven
authors.initials: S
authors.lastname: Dessein
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Motley
authors.forename: Birgitta
authors.initials: B
authors.lastname: Bremer
mesh_terms: D001499:Bayes Theorem; D002736:Chloroplasts / Q000235:genetics; D018742:DNA, Chloroplast / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D019143:Evolution, Molecular; D005819:Genetic Markers; D018745:Genome, Plant; D007438:Introns; D008390:Markov Chains; D008957:Models, Genetic; D009010:Monte Carlo Method; D010802:Phylogeny; D019666:Rubiaceae / Q000145:classification / Q000235:genetics*; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D018742:DNA, Chloroplast; D018744:DNA, Plant; D021903:DNA, Ribosomal Spacer; D005819:Genetic Markers